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Stockwell J, Daniels AD, Windle CL, Harman TA, Woodhall T, Lebl T, Trinh CH, Mulholland K, Pearson AR, Berry A, Nelson A. Evaluation of fluoropyruvate as nucleophile in reactions catalysed by N-acetyl neuraminic acid lyase variants: scope, limitations and stereoselectivity. Org Biomol Chem 2016; 14:105-12. [PMID: 26537532 PMCID: PMC4717870 DOI: 10.1039/c5ob02037a] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 10/30/2015] [Indexed: 12/25/2022]
Abstract
The catalysis of reactions involving fluoropyruvate as donor by N-acetyl neuraminic acid lyase (NAL) variants was investigated. Under kinetic control, the wild-type enzyme catalysed the reaction between fluoropyruvate and N-acetyl mannosamine to give a 90 : 10 ratio of the (3R,4R)- and (3S,4R)-configured products; after extended reaction times, equilibration occurred to give a 30 : 70 mixture of these products. The efficiency and stereoselectivity of reactions of a range of substrates catalysed by the E192N, E192N/T167V/S208V and E192N/T167G NAL variants were also studied. Using fluoropyruvate and (2R,3S)- or (2S,3R)-2,3-dihydroxy-4-oxo-N,N-dipropylbutanamide as substrates, it was possible to obtain three of the four possible diastereomeric products; for each product, the ratio of anomeric and pyranose/furanose forms was determined. The crystal structure of S. aureus NAL in complex with fluoropyruvate was determined, assisting rationalisation of the stereochemical outcome of C-C bond formation.
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Affiliation(s)
- Jennifer Stockwell
- School of Chemistry , University of Leeds , Leeds , LS2 9JT , UK .
- Astbury Centre for Structural Molecular Biology , University of Leeds , Leeds , LS2 9JT , UK .
| | - Adam D. Daniels
- Astbury Centre for Structural Molecular Biology , University of Leeds , Leeds , LS2 9JT , UK .
- School of Molecular and Cellular Biology , University of Leeds , Leeds , LS2 9JT , UK
| | - Claire L. Windle
- Astbury Centre for Structural Molecular Biology , University of Leeds , Leeds , LS2 9JT , UK .
- School of Molecular and Cellular Biology , University of Leeds , Leeds , LS2 9JT , UK
| | - Thomas A. Harman
- School of Chemistry , University of Leeds , Leeds , LS2 9JT , UK .
- Astbury Centre for Structural Molecular Biology , University of Leeds , Leeds , LS2 9JT , UK .
| | - Thomas Woodhall
- School of Chemistry , University of Leeds , Leeds , LS2 9JT , UK .
- Astbury Centre for Structural Molecular Biology , University of Leeds , Leeds , LS2 9JT , UK .
| | - Tomas Lebl
- School of Chemistry , University of St Andrews , St Andrews , KY16 9ST , UK
| | - Chi H. Trinh
- Astbury Centre for Structural Molecular Biology , University of Leeds , Leeds , LS2 9JT , UK .
- School of Molecular and Cellular Biology , University of Leeds , Leeds , LS2 9JT , UK
| | - Keith Mulholland
- Chemical Development , AstraZeneca , Silk Road Business Park , Macclesfield , Cheshire , SK10 2NA , UK
| | - Arwen R. Pearson
- Astbury Centre for Structural Molecular Biology , University of Leeds , Leeds , LS2 9JT , UK .
- School of Molecular and Cellular Biology , University of Leeds , Leeds , LS2 9JT , UK
| | - Alan Berry
- Astbury Centre for Structural Molecular Biology , University of Leeds , Leeds , LS2 9JT , UK .
- School of Molecular and Cellular Biology , University of Leeds , Leeds , LS2 9JT , UK
| | - Adam Nelson
- School of Chemistry , University of Leeds , Leeds , LS2 9JT , UK .
- Astbury Centre for Structural Molecular Biology , University of Leeds , Leeds , LS2 9JT , UK .
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Daniels AD, Campeotto I, van der Kamp MW, Bolt AH, Trinh CH, Phillips SEV, Pearson A, Nelson A, Mulholland AJ, Berry A. Reaction mechanism of N-acetylneuraminic acid lyase revealed by a combination of crystallography, QM/MM simulation, and mutagenesis. ACS Chem Biol 2014; 9:1025-32. [PMID: 24521460 PMCID: PMC4004234 DOI: 10.1021/cb500067z] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
N-Acetylneuraminic acid lyase (NAL) is a Class I aldolase that catalyzes the reversible condensation of pyruvate with N-acetyl-d-mannosamine (ManNAc) to yield the sialic acid N-acetylneuraminic acid (Neu5Ac). Aldolases are finding increasing use as biocatalysts for the stereospecific synthesis of complex molecules. Incomplete understanding of the mechanism of catalysis in aldolases, however, can hamper development of new enzyme activities and specificities, including control over newly generated stereocenters. In the case of NAL, it is clear that the enzyme catalyzes a Bi-Uni ordered condensation reaction in which pyruvate binds first to the enzyme to form a catalytically important Schiff base. The identity of the residues required for catalysis of the condensation step and the nature of the transition state for this reaction, however, have been a matter of conjecture. In order to address, this we crystallized a Y137A variant of the E. coli NAL in the presence of Neu5Ac. The three-dimensional structure shows a full length sialic acid bound in the active site of subunits A, B, and D, while in subunit C, discontinuous electron density reveals the positions of enzyme-bound pyruvate and ManNAc. These 'snapshot' structures, representative of intermediates in the enzyme catalytic cycle, provided an ideal starting point for QM/MM modeling of the enzymic reaction of carbon-carbon bond formation. This revealed that Tyr137 acts as the proton donor to the aldehyde oxygen of ManNAc during the reaction, the activation barrier is dominated by carbon-carbon bond formation, and proton transfer from Tyr137 is required to obtain a stable Neu5Ac-Lys165 Schiff base complex. The results also suggested that a triad of residues, Tyr137, Ser47, and Tyr110 from a neighboring subunit, are required to correctly position Tyr137 for its function, and this was confirmed by site-directed mutagenesis. This understanding of the mechanism and geometry of the transition states along the C-C bond-forming pathway will allow further development of these enzymes for stereospecific synthesis of new enzyme products.
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Affiliation(s)
- Adam D. Daniels
- Astbury Centre for
Structural Molecular Biology and School of Molecular and Cellular
Biology, University of Leeds, Leeds LS2 9JT, U.K.
| | - Ivan Campeotto
- Astbury Centre for
Structural Molecular Biology and School of Molecular and Cellular
Biology, University of Leeds, Leeds LS2 9JT, U.K.
| | - Marc W. van der Kamp
- Centre for Computational Chemistry, School
of Chemistry, University of Bristol, Bristol BS8 1TS, U.K.
| | - Amanda H. Bolt
- Astbury Centre for
Structural Molecular Biology and School of Molecular and Cellular
Biology, University of Leeds, Leeds LS2 9JT, U.K.
| | - Chi H. Trinh
- Astbury Centre for
Structural Molecular Biology and School of Molecular and Cellular
Biology, University of Leeds, Leeds LS2 9JT, U.K.
| | - Simon E. V. Phillips
- Astbury Centre for
Structural Molecular Biology and School of Molecular and Cellular
Biology, University of Leeds, Leeds LS2 9JT, U.K.
| | - Arwen
R. Pearson
- Astbury Centre for
Structural Molecular Biology and School of Molecular and Cellular
Biology, University of Leeds, Leeds LS2 9JT, U.K.
| | - Adam Nelson
- Astbury Centre for Structural Molecular
Biology and School of Chemistry, University
of Leeds, Leeds LS2 9JT, U.K.
| | - Adrian J. Mulholland
- Centre for Computational Chemistry, School
of Chemistry, University of Bristol, Bristol BS8 1TS, U.K.,E-mail:
| | - Alan Berry
- Astbury Centre for
Structural Molecular Biology and School of Molecular and Cellular
Biology, University of Leeds, Leeds LS2 9JT, U.K.,E-mail:
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McLellan SL, Daniels AD, Salmore AK. Clonal populations of thermotolerant Enterobacteriaceae in recreational water and their potential interference with fecal Escherichia coli counts. Appl Environ Microbiol 2001; 67:4934-8. [PMID: 11571207 PMCID: PMC93254 DOI: 10.1128/aem.67.10.4934-4938.2001] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacterial strains were isolated from beach water samples using the original Environmental Protection Agency method for Escherichia coli enumeration and analyzed by pulsed-field gel electrophoresis (PFGE). Identical PFGE patterns were found for numerous isolates from 4 of the 9 days sampled, suggesting environmental replication. 16S rRNA gene sequencing, API 20E biochemical testing, and the absence of beta-glucuronidase activity revealed that these clonal isolates were Klebsiella, Citrobacter, and Enterobacter spp. In contrast, 82% of the nonclonal isolates from water samples were confirmed to be E. coli, and 16% were identified as other fecal coliforms. These nonclonal isolates produced a diverse range of PFGE patterns similar to those of isolates obtained directly from untreated sewage and gull droppings. beta-Glucuronidase activity was critical in distinguishing E. coli from other fecal coliforms, particularly for the clonal isolates. These findings demonstrate that E. coli is a better indicator of fecal pollution than fecal coliforms, which may replicate in the environment and falsely elevate indicator organism levels.
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Affiliation(s)
- S L McLellan
- Great Lakes WATER Institute, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin 53204, USA.
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